{"gene":"ANKRD9","run_date":"2026-04-28T17:12:37","timeline":{"discoveries":[{"year":2018,"finding":"ANKRD9 functions as a substrate receptor subunit of a CRL5 E3 ubiquitin ligase complex, assembling with CUL5, ELOB, ELOC, and RNF7, and directly binding IMPDH1 and IMPDH2 to promote their ubiquitination and proteasomal degradation.","method":"Quantitative proteomics, western blotting, complex reconstitution assays, in vitro ubiquitylation assay, knockdown with proliferation readouts","journal":"Biochimica et biophysica acta. Molecular basis of disease","confidence":"High","confidence_rationale":"Tier 1 — in vitro ubiquitylation assay + reconstitution + multiple orthogonal methods in a single study","pmids":["30293565"],"is_preprint":false},{"year":2019,"finding":"ANKRD9 facilitates degradation of IMPDH2 under basal conditions; upon nutrient limitation, ANKRD9 transitions from vesicle-like structures to co-assemble with IMPDH2 into rod-like filaments where IMPDH2 is stable. Inhibition of IMPDH2 activity with ribavirin favors ANKRD9 binding to IMPDH2 rods, and guanosine reverses rod formation. The conserved Cys109-Cys110 motif in ANKRD9 is required for the vesicle-to-rods transition and for binding and regulation of IMPDH2.","method":"Live-cell fluorescence imaging, ANKRD9 knockdown and overexpression, ribavirin and guanosine pharmacological perturbations, site-directed mutagenesis of Cys109/Cys110","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — mutagenesis + imaging + pharmacological rescue, multiple orthogonal methods in single study","pmids":["31337707"],"is_preprint":false},{"year":2009,"finding":"ANKRD9 protein localizes to the cytoplasm as shown by GFP-tagging, and its mRNA is regulated by metabolic perturbations including fatty acid oxidation defects, thyroid hormone, fasting, re-feeding, and apoptosis, pointing to a role in intracellular lipid metabolism.","method":"Transient transfection of GFP-tagged ANKRD9 (subcellular localization), qRT-PCR in lipid-perturbed models","journal":"BMB reports","confidence":"Medium","confidence_rationale":"Tier 3 — single-lab localization by GFP tagging without functional mutagenesis follow-up","pmids":["19788857"],"is_preprint":false},{"year":2026,"finding":"ANKRD9 couples ATP synthesis with lipoprotein trafficking in enterocytes: it regulates enzymes in the purine biosynthesis/salvage pathway to increase ATP, and its intracellular localization is lipid- and ATP-dependent. Inactivation of Ankrd9 in mice reduces intestinal ATP, alters Golgi morphology, delays ApoB/chylomicron trafficking, and causes lipid accumulation in enterocytes and a lean body phenotype.","method":"Ankrd9 knockout mouse model, intestinal ATP measurements, Golgi morphology imaging, ApoB/chylomicron trafficking assay, metabolic phenotyping","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — in vivo KO with multiple defined cellular and metabolic phenotypes plus mechanistic pathway placement","pmids":["41826336"],"is_preprint":false},{"year":2026,"finding":"In chicken myoblasts, ANKRD9 directly binds IMPDH2 and promotes its ubiquitin-mediated degradation without affecting IMPDH2 mRNA levels; ANKRD9 overexpression inhibits myoblast proliferation and differentiation, and restoring IMPDH2 expression rescues these inhibitory effects. In vivo siRNA-mediated knockdown of ANKRD9 increases muscle mass and myofiber diameter.","method":"Co-immunoprecipitation (direct binding), ubiquitination assay, overexpression/knockdown, rescue experiments, in vivo siRNA knockdown","journal":"Poultry science","confidence":"Medium","confidence_rationale":"Tier 2 — direct binding + ubiquitination assay + in vivo rescue, but in chicken (ortholog context)","pmids":["41691811"],"is_preprint":false},{"year":2021,"finding":"miR-29b-1-5p directly binds the 3'UTR of ANKRD9 mRNA and suppresses ANKRD9 expression in chicken primary myoblasts, placing ANKRD9 as a downstream target of miR-29b-1-5p in muscle development.","method":"Luciferase 3'UTR reporter assay, western blotting","journal":"Poultry science","confidence":"Medium","confidence_rationale":"Tier 3 — 3'UTR binding validated by reporter assay, single lab","pmids":["34852967"],"is_preprint":false}],"current_model":"ANKRD9 is a metabolically-regulated ankyrin repeat protein that acts as a substrate receptor subunit of a CUL5-RING E3 ubiquitin ligase complex (with ELOB, ELOC, RNF7) to ubiquitinate and degrade IMPDH2 (and IMPDH1); under nutrient-limiting conditions it transitions from cytoplasmic vesicle-like structures to co-assemble with IMPDH2 into stabilizing rod-like filaments via its Cys109-Cys110 motif, and in enterocytes it additionally couples purine biosynthesis/ATP production to Golgi dynamics and chylomicron trafficking, with its intracellular localization being lipid- and ATP-dependent."},"narrative":{"teleology":[{"year":2009,"claim":"Establishing that ANKRD9 is a metabolically responsive gene resolved its initial biological context: its transcript levels change with fatty acid oxidation defects, thyroid hormone, and fasting/refeeding, implicating it in lipid/energy metabolism before any molecular function was known.","evidence":"qRT-PCR in lipid-perturbed mouse models and GFP-tagged localization in transfected cells","pmids":["19788857"],"confidence":"Medium","gaps":["Single-lab GFP overexpression without endogenous localization confirmation","No direct functional assay or binding partner identified","Mechanism linking metabolic transcriptional regulation to protein function unknown"]},{"year":2018,"claim":"Identifying ANKRD9 as a CRL5 substrate receptor that directly binds and ubiquitinates IMPDH1/2 established its first molecular function, explaining how it controls purine nucleotide metabolism at the post-translational level.","evidence":"Quantitative proteomics, reconstituted CUL5–ELOB–ELOC–RNF7 complex, in vitro ubiquitylation assay, knockdown with proliferation readouts in human cells","pmids":["30293565"],"confidence":"High","gaps":["Structural basis of ANKRD9–IMPDH2 recognition unresolved","Whether ANKRD9 targets additional substrates beyond IMPDH1/2 not tested","Physiological signals controlling ANKRD9 E3 ligase activity not defined"]},{"year":2019,"claim":"Demonstrating that ANKRD9 switches from vesicle-like puncta to IMPDH2-stabilizing rod filaments under nutrient limitation revealed a metabolite-sensitive regulatory mechanism, showing that ANKRD9 can toggle between degrading and protecting its substrate depending on cellular metabolic state.","evidence":"Live-cell fluorescence imaging, ribavirin/guanosine pharmacological perturbation, Cys109/Cys110 site-directed mutagenesis in cultured cells","pmids":["31337707"],"confidence":"High","gaps":["Molecular trigger (specific metabolite or redox state) that initiates the vesicle-to-rod transition not identified","Whether the Cys109–Cys110 motif functions via disulfide bonding or another chemistry not resolved","Structural organization of ANKRD9 within IMPDH2 rods unknown"]},{"year":2021,"claim":"Showing that miR-29b-1-5p directly targets the ANKRD9 3′UTR to suppress its expression placed ANKRD9 within a post-transcriptional regulatory circuit in muscle development.","evidence":"Luciferase 3′UTR reporter assay and western blotting in chicken primary myoblasts","pmids":["34852967"],"confidence":"Medium","gaps":["Single-lab finding in chicken myoblasts; conservation in mammals not tested","Functional consequences of miR-29b-1-5p–mediated ANKRD9 suppression on IMPDH2 levels not assessed","Whether this regulatory axis operates in vivo during muscle growth not demonstrated"]},{"year":2026,"claim":"In vivo knockout of Ankrd9 in mice revealed its physiological role in coupling purine biosynthesis/ATP production to Golgi integrity and chylomicron secretion in enterocytes, connecting its E3 ligase function to whole-organism lipid metabolism and body composition.","evidence":"Ankrd9 knockout mouse, intestinal ATP quantification, Golgi morphology imaging, ApoB/chylomicron trafficking assays, metabolic phenotyping","pmids":["41826336"],"confidence":"High","gaps":["Whether the Golgi phenotype is a direct consequence of IMPDH2 mis-regulation or involves additional substrates not established","Tissue-specific contributions beyond enterocytes (e.g. liver, muscle) not dissected in this study","Lipid- and ATP-dependent localization signals on ANKRD9 protein not mapped"]},{"year":2026,"claim":"Confirming the ANKRD9–IMPDH2 ubiquitination axis in a non-mammalian vertebrate (chicken) and linking it to myoblast proliferation and muscle mass broadened the functional scope and demonstrated evolutionary conservation of the pathway.","evidence":"Co-immunoprecipitation, ubiquitination assay, overexpression/knockdown with IMPDH2 rescue, in vivo siRNA knockdown in chicken","pmids":["41691811"],"confidence":"Medium","gaps":["Cross-species validation in mammalian muscle not performed","Whether ANKRD9's effect on muscle differentiation is entirely IMPDH2-dependent or involves other substrates not fully excluded","Mechanism by which purine nucleotide levels regulate myoblast differentiation downstream not defined"]},{"year":null,"claim":"Key unresolved questions include the structural basis of ANKRD9–IMPDH2 recognition, the identity of the metabolite or redox signal triggering the vesicle-to-rod transition, whether ANKRD9 ubiquitinates substrates beyond IMPDH1/2, and the tissue-specific physiological roles outside the intestine.","evidence":"","pmids":[],"confidence":"Low","gaps":["No crystal or cryo-EM structure of ANKRD9 or its complex with IMPDH2","Full substrate repertoire of the ANKRD9–CRL5 complex not systematically surveyed","Tissue-specific conditional knockout studies beyond intestine not reported"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,4]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[1]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[1]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,4]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[3]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[3]}],"complexes":["CRL5 (CUL5–ELOB–ELOC–RNF7–ANKRD9)"],"partners":["CUL5","ELOB","ELOC","RNF7","IMPDH2","IMPDH1"],"other_free_text":[]},"mechanistic_narrative":"ANKRD9 is a metabolically regulated ankyrin repeat protein that functions as a substrate receptor of a CUL5–ELOB–ELOC–RNF7 E3 ubiquitin ligase complex, directly binding IMPDH1 and IMPDH2 to promote their ubiquitination and proteasomal degradation, thereby controlling purine nucleotide biosynthesis [PMID:30293565, PMID:41691811]. Under nutrient-limiting conditions, ANKRD9 transitions from cytoplasmic vesicle-like structures to co-assemble with IMPDH2 into stabilizing rod-like filaments via its conserved Cys109–Cys110 motif, a switch that is reversed by guanosine supplementation [PMID:31337707]. In intestinal enterocytes, ANKRD9 couples purine biosynthesis and ATP production to Golgi dynamics and chylomicron trafficking; Ankrd9 knockout in mice reduces intestinal ATP, disrupts Golgi morphology, delays ApoB/chylomicron secretion, and produces a lean phenotype with enterocyte lipid accumulation [PMID:41826336]. ANKRD9 expression is itself regulated by metabolic cues including fatty acid oxidation status, thyroid hormone, and fasting–refeeding cycles [PMID:19788857]."},"prefetch_data":{"uniprot":{"accession":"Q96BM1","full_name":"Ankyrin repeat domain-containing protein 9","aliases":[],"length_aa":317,"mass_kda":34.3,"function":"Substrate receptor subunit of a cullin-RING superfamily E3 ligase complex (CUL5-based E3 ubiquitin ligase complex) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:30293565). Depending of the metabolic state of the cell, promotes the proteasomal degradation of IMPDH2, the rate-limiting enzyme in GTP biosynthesis or protects IMPDH2 by stabilizing IMPDH2 filaments assembly (PubMed:30293565, PubMed:31337707). Implicated in different cellular processes, like copper homeostasis and cell proliferation (PubMed:24522796, PubMed:30293565)","subcellular_location":"Cytoplasmic vesicle; Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/Q96BM1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ANKRD9","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ANKRD9","total_profiled":1310},"omim":[{"mim_id":"618605","title":"ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 9; ANKRD9","url":"https://www.omim.org/entry/618605"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"heart muscle","ntpm":104.9},{"tissue":"skeletal muscle","ntpm":148.8}],"url":"https://www.proteinatlas.org/search/ANKRD9"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q96BM1","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96BM1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96BM1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96BM1-F1-predicted_aligned_error_v6.png","plddt_mean":81.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ANKRD9","jax_strain_url":"https://www.jax.org/strain/search?query=ANKRD9"},"sequence":{"accession":"Q96BM1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96BM1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96BM1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96BM1"}},"corpus_meta":[{"pmid":"29618728","id":"PMC_29618728","title":"Association between DNA methylation in cord blood and maternal smoking: The Hokkaido Study on Environment and Children's Health.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29618728","citation_count":36,"is_preprint":false},{"pmid":"35798818","id":"PMC_35798818","title":"EWAS of post-COVID-19 patients shows methylation differences in the immune-response associated gene, IFI44L, three months after COVID-19 infection.","date":"2022","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/35798818","citation_count":23,"is_preprint":false},{"pmid":"31337707","id":"PMC_31337707","title":"ANKRD9 is a metabolically-controlled regulator of IMPDH2 abundance and macro-assembly.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31337707","citation_count":22,"is_preprint":false},{"pmid":"30293565","id":"PMC_30293565","title":"ANKRD9 is associated with tumor suppression as a substrate receptor subunit of ubiquitin ligase.","date":"2018","source":"Biochimica et biophysica acta. Molecular basis of disease","url":"https://pubmed.ncbi.nlm.nih.gov/30293565","citation_count":20,"is_preprint":false},{"pmid":"34852967","id":"PMC_34852967","title":"MiR-29b-1-5p regulates the proliferation and differentiation of chicken primary myoblasts and analysis of its effective targets.","date":"2021","source":"Poultry science","url":"https://pubmed.ncbi.nlm.nih.gov/34852967","citation_count":17,"is_preprint":false},{"pmid":"19788857","id":"PMC_19788857","title":"Regulation of ANKRD9 expression by lipid metabolic perturbations.","date":"2009","source":"BMB reports","url":"https://pubmed.ncbi.nlm.nih.gov/19788857","citation_count":16,"is_preprint":false},{"pmid":"38900908","id":"PMC_38900908","title":"Embryonic alcohol exposure in zebrafish predisposes adults to cardiomyopathy and diastolic dysfunction.","date":"2024","source":"Cardiovascular research","url":"https://pubmed.ncbi.nlm.nih.gov/38900908","citation_count":5,"is_preprint":false},{"pmid":"35928108","id":"PMC_35928108","title":"Mechanism of Lysoforte in Improving Jejuna Morphology and Health in Broiler Chickens.","date":"2022","source":"Frontiers in veterinary science","url":"https://pubmed.ncbi.nlm.nih.gov/35928108","citation_count":2,"is_preprint":false},{"pmid":"41769753","id":"PMC_41769753","title":"Integrative 'omics' analysis elucidates the role of the gene ANKRD9 in modulating chicken primary myoblast IMP metabolism via the purine metabolic pathway.","date":"2026","source":"British poultry science","url":"https://pubmed.ncbi.nlm.nih.gov/41769753","citation_count":0,"is_preprint":false},{"pmid":"41691811","id":"PMC_41691811","title":"ANKRD9 negatively regulates chicken myogenesis through ubiquitin-mediated regulation of IMPDH2.","date":"2026","source":"Poultry science","url":"https://pubmed.ncbi.nlm.nih.gov/41691811","citation_count":0,"is_preprint":false},{"pmid":"41826336","id":"PMC_41826336","title":"Enterocytes rely on purine biosynthesis/salvage pathway to facilitate dietary fat absorption.","date":"2026","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/41826336","citation_count":0,"is_preprint":false},{"pmid":"41940665","id":"PMC_41940665","title":"Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.","date":"2026","source":"Microbiology spectrum","url":"https://pubmed.ncbi.nlm.nih.gov/41940665","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7536,"output_tokens":1648,"usd":0.023664},"stage2":{"model":"claude-opus-4-6","input_tokens":4884,"output_tokens":2279,"usd":0.122093},"total_usd":0.145757,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"ANKRD9 functions as a substrate receptor subunit of a CRL5 E3 ubiquitin ligase complex, assembling with CUL5, ELOB, ELOC, and RNF7, and directly binding IMPDH1 and IMPDH2 to promote their ubiquitination and proteasomal degradation.\",\n      \"method\": \"Quantitative proteomics, western blotting, complex reconstitution assays, in vitro ubiquitylation assay, knockdown with proliferation readouts\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular basis of disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro ubiquitylation assay + reconstitution + multiple orthogonal methods in a single study\",\n      \"pmids\": [\"30293565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ANKRD9 facilitates degradation of IMPDH2 under basal conditions; upon nutrient limitation, ANKRD9 transitions from vesicle-like structures to co-assemble with IMPDH2 into rod-like filaments where IMPDH2 is stable. Inhibition of IMPDH2 activity with ribavirin favors ANKRD9 binding to IMPDH2 rods, and guanosine reverses rod formation. The conserved Cys109-Cys110 motif in ANKRD9 is required for the vesicle-to-rods transition and for binding and regulation of IMPDH2.\",\n      \"method\": \"Live-cell fluorescence imaging, ANKRD9 knockdown and overexpression, ribavirin and guanosine pharmacological perturbations, site-directed mutagenesis of Cys109/Cys110\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — mutagenesis + imaging + pharmacological rescue, multiple orthogonal methods in single study\",\n      \"pmids\": [\"31337707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"ANKRD9 protein localizes to the cytoplasm as shown by GFP-tagging, and its mRNA is regulated by metabolic perturbations including fatty acid oxidation defects, thyroid hormone, fasting, re-feeding, and apoptosis, pointing to a role in intracellular lipid metabolism.\",\n      \"method\": \"Transient transfection of GFP-tagged ANKRD9 (subcellular localization), qRT-PCR in lipid-perturbed models\",\n      \"journal\": \"BMB reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single-lab localization by GFP tagging without functional mutagenesis follow-up\",\n      \"pmids\": [\"19788857\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ANKRD9 couples ATP synthesis with lipoprotein trafficking in enterocytes: it regulates enzymes in the purine biosynthesis/salvage pathway to increase ATP, and its intracellular localization is lipid- and ATP-dependent. Inactivation of Ankrd9 in mice reduces intestinal ATP, alters Golgi morphology, delays ApoB/chylomicron trafficking, and causes lipid accumulation in enterocytes and a lean body phenotype.\",\n      \"method\": \"Ankrd9 knockout mouse model, intestinal ATP measurements, Golgi morphology imaging, ApoB/chylomicron trafficking assay, metabolic phenotyping\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo KO with multiple defined cellular and metabolic phenotypes plus mechanistic pathway placement\",\n      \"pmids\": [\"41826336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In chicken myoblasts, ANKRD9 directly binds IMPDH2 and promotes its ubiquitin-mediated degradation without affecting IMPDH2 mRNA levels; ANKRD9 overexpression inhibits myoblast proliferation and differentiation, and restoring IMPDH2 expression rescues these inhibitory effects. In vivo siRNA-mediated knockdown of ANKRD9 increases muscle mass and myofiber diameter.\",\n      \"method\": \"Co-immunoprecipitation (direct binding), ubiquitination assay, overexpression/knockdown, rescue experiments, in vivo siRNA knockdown\",\n      \"journal\": \"Poultry science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct binding + ubiquitination assay + in vivo rescue, but in chicken (ortholog context)\",\n      \"pmids\": [\"41691811\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"miR-29b-1-5p directly binds the 3'UTR of ANKRD9 mRNA and suppresses ANKRD9 expression in chicken primary myoblasts, placing ANKRD9 as a downstream target of miR-29b-1-5p in muscle development.\",\n      \"method\": \"Luciferase 3'UTR reporter assay, western blotting\",\n      \"journal\": \"Poultry science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — 3'UTR binding validated by reporter assay, single lab\",\n      \"pmids\": [\"34852967\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ANKRD9 is a metabolically-regulated ankyrin repeat protein that acts as a substrate receptor subunit of a CUL5-RING E3 ubiquitin ligase complex (with ELOB, ELOC, RNF7) to ubiquitinate and degrade IMPDH2 (and IMPDH1); under nutrient-limiting conditions it transitions from cytoplasmic vesicle-like structures to co-assemble with IMPDH2 into stabilizing rod-like filaments via its Cys109-Cys110 motif, and in enterocytes it additionally couples purine biosynthesis/ATP production to Golgi dynamics and chylomicron trafficking, with its intracellular localization being lipid- and ATP-dependent.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ANKRD9 is a metabolically regulated ankyrin repeat protein that functions as a substrate receptor of a CUL5–ELOB–ELOC–RNF7 E3 ubiquitin ligase complex, directly binding IMPDH1 and IMPDH2 to promote their ubiquitination and proteasomal degradation, thereby controlling purine nucleotide biosynthesis [PMID:30293565, PMID:41691811]. Under nutrient-limiting conditions, ANKRD9 transitions from cytoplasmic vesicle-like structures to co-assemble with IMPDH2 into stabilizing rod-like filaments via its conserved Cys109–Cys110 motif, a switch that is reversed by guanosine supplementation [PMID:31337707]. In intestinal enterocytes, ANKRD9 couples purine biosynthesis and ATP production to Golgi dynamics and chylomicron trafficking; Ankrd9 knockout in mice reduces intestinal ATP, disrupts Golgi morphology, delays ApoB/chylomicron secretion, and produces a lean phenotype with enterocyte lipid accumulation [PMID:41826336]. ANKRD9 expression is itself regulated by metabolic cues including fatty acid oxidation status, thyroid hormone, and fasting–refeeding cycles [PMID:19788857].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Establishing that ANKRD9 is a metabolically responsive gene resolved its initial biological context: its transcript levels change with fatty acid oxidation defects, thyroid hormone, and fasting/refeeding, implicating it in lipid/energy metabolism before any molecular function was known.\",\n      \"evidence\": \"qRT-PCR in lipid-perturbed mouse models and GFP-tagged localization in transfected cells\",\n      \"pmids\": [\"19788857\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab GFP overexpression without endogenous localization confirmation\",\n        \"No direct functional assay or binding partner identified\",\n        \"Mechanism linking metabolic transcriptional regulation to protein function unknown\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identifying ANKRD9 as a CRL5 substrate receptor that directly binds and ubiquitinates IMPDH1/2 established its first molecular function, explaining how it controls purine nucleotide metabolism at the post-translational level.\",\n      \"evidence\": \"Quantitative proteomics, reconstituted CUL5–ELOB–ELOC–RNF7 complex, in vitro ubiquitylation assay, knockdown with proliferation readouts in human cells\",\n      \"pmids\": [\"30293565\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of ANKRD9–IMPDH2 recognition unresolved\",\n        \"Whether ANKRD9 targets additional substrates beyond IMPDH1/2 not tested\",\n        \"Physiological signals controlling ANKRD9 E3 ligase activity not defined\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that ANKRD9 switches from vesicle-like puncta to IMPDH2-stabilizing rod filaments under nutrient limitation revealed a metabolite-sensitive regulatory mechanism, showing that ANKRD9 can toggle between degrading and protecting its substrate depending on cellular metabolic state.\",\n      \"evidence\": \"Live-cell fluorescence imaging, ribavirin/guanosine pharmacological perturbation, Cys109/Cys110 site-directed mutagenesis in cultured cells\",\n      \"pmids\": [\"31337707\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular trigger (specific metabolite or redox state) that initiates the vesicle-to-rod transition not identified\",\n        \"Whether the Cys109–Cys110 motif functions via disulfide bonding or another chemistry not resolved\",\n        \"Structural organization of ANKRD9 within IMPDH2 rods unknown\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showing that miR-29b-1-5p directly targets the ANKRD9 3′UTR to suppress its expression placed ANKRD9 within a post-transcriptional regulatory circuit in muscle development.\",\n      \"evidence\": \"Luciferase 3′UTR reporter assay and western blotting in chicken primary myoblasts\",\n      \"pmids\": [\"34852967\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab finding in chicken myoblasts; conservation in mammals not tested\",\n        \"Functional consequences of miR-29b-1-5p–mediated ANKRD9 suppression on IMPDH2 levels not assessed\",\n        \"Whether this regulatory axis operates in vivo during muscle growth not demonstrated\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"In vivo knockout of Ankrd9 in mice revealed its physiological role in coupling purine biosynthesis/ATP production to Golgi integrity and chylomicron secretion in enterocytes, connecting its E3 ligase function to whole-organism lipid metabolism and body composition.\",\n      \"evidence\": \"Ankrd9 knockout mouse, intestinal ATP quantification, Golgi morphology imaging, ApoB/chylomicron trafficking assays, metabolic phenotyping\",\n      \"pmids\": [\"41826336\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether the Golgi phenotype is a direct consequence of IMPDH2 mis-regulation or involves additional substrates not established\",\n        \"Tissue-specific contributions beyond enterocytes (e.g. liver, muscle) not dissected in this study\",\n        \"Lipid- and ATP-dependent localization signals on ANKRD9 protein not mapped\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Confirming the ANKRD9–IMPDH2 ubiquitination axis in a non-mammalian vertebrate (chicken) and linking it to myoblast proliferation and muscle mass broadened the functional scope and demonstrated evolutionary conservation of the pathway.\",\n      \"evidence\": \"Co-immunoprecipitation, ubiquitination assay, overexpression/knockdown with IMPDH2 rescue, in vivo siRNA knockdown in chicken\",\n      \"pmids\": [\"41691811\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Cross-species validation in mammalian muscle not performed\",\n        \"Whether ANKRD9's effect on muscle differentiation is entirely IMPDH2-dependent or involves other substrates not fully excluded\",\n        \"Mechanism by which purine nucleotide levels regulate myoblast differentiation downstream not defined\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of ANKRD9–IMPDH2 recognition, the identity of the metabolite or redox signal triggering the vesicle-to-rod transition, whether ANKRD9 ubiquitinates substrates beyond IMPDH1/2, and the tissue-specific physiological roles outside the intestine.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No crystal or cryo-EM structure of ANKRD9 or its complex with IMPDH2\",\n        \"Full substrate repertoire of the ANKRD9–CRL5 complex not systematically surveyed\",\n        \"Tissue-specific conditional knockout studies beyond intestine not reported\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\n      \"CRL5 (CUL5–ELOB–ELOC–RNF7–ANKRD9)\"\n    ],\n    \"partners\": [\n      \"CUL5\",\n      \"ELOB\",\n      \"ELOC\",\n      \"RNF7\",\n      \"IMPDH2\",\n      \"IMPDH1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}